Influence of membrane composition on the binding and folding of a membrane lytic peptide from the non-enveloped flock house virus

Abstract

Using a combination of coarse-grained and atomistic molecular dynamics simulations we have investigated the membrane binding and folding properties of the membrane lytic peptide of Flock House virus (FHV). FHV is an animal virus and an excellent model system for studying cell entry mechanisms in non-enveloped viruses. FHV undergoes a maturation event where the 44 C-terminal amino acids are cleaved from the major capsid protein, forming the membrane lytic (γ) peptides. Under acidic conditions, γ is released from the capsid interior allowing the peptides to bind and disrupt membranes. The first 21 N-terminal residues of γ, termed γ1, have been resolved in the FHV capsid structure and γ1 has been the subject of in vitro studies. γ1 is structurally dynamic as it adopts helical secondary structure inside the capsid and on membranes, but it is disordered in solution. In vitro studies have shown the binding free energies to POPC or POPG membranes are nearly equivalent, but binding to POPC is enthalpically driven, while POPG binding is entropically driven. Through coarse-grained and multiple microsecond all-atom simulations the membrane binding and folding properties of γ1 are investigated against homogeneous and heterogeneous bilayers to elucidate the dependence of the microenvironment on the structural properties of γ1. Our studies provide a rationale for the thermodynamic data and suggest binding of γ1 to POPG bilayers occurs in a disordered state, but γ1 must adopt a helical conformation when binding POPC bilayers.

The RNA Capping Enzyme Domain in Protein A is Essential for Flock House Virus Replication

“…Flock house virus (FHV), a member of the family Nodaviridae , was first isolated from a grass grub ( Costelytra zealandica ) in New Zealand [ 1 ]. It is a small non-enveloped virus comprising an icosahedral protein capsid and a single-stranded RNA genome of positive polarity [ 2 , 3 ]. Studies on FHV infection and the replication of its genome have provided valuable insights about virus entry and assembly [ 3 ], and antiviral immune response [ 4 ].…”

Folding a viral peptide in different membrane environments: pathway and sampling analyses

“…We found that γ 1 does not unfold and remains embedded in the membranes throughout 1-μs simulations. From these observations, we proposed that an energy barrier separates the folded state from the low helicity state, and the barrier height has a dependence on the amount of charge in the membrane [37]. Our equilibrium simulations were likely trapped in a metastable state, due to the rough energy landscape, which was insurmountable by conventional simulation approaches.…”

“…In our previous work [37], we investigated the thermodynamic aspects of binding and the structural dynamics of the FHV 21 N-terminal residues of the γ peptide (known as γ 1 ) using a multi-scale approach. We examined the binding and folding characteristics of γ 1 on pure phosphatidylcholine (PC), pure phosphatidylglycerol (PG) and a 50:50 mixed PC:PG membrane.…”

“…Umbrella sampling is a mature and heavily utilized method in different biophysics studies including protein folding [49,50], peptide-peptide interactions [51,52], protein-DNA interactions [53], binding energies and interactions with lipid membranes [20,37,54,55], and conformational sampling of small molecules [56,57], among others. US relies on a stratification strategy; intermediate states along an order parameter are simulated with a restraint potential that keeps the system localized to a chosen point along the order parameter.…”

“…Many non-enveloped viruses [58,59] contain a membrane active component of their capsid that in some systems is an amphipathic peptide, which is disconnected from the capsid. We have been investigating the membrane lytic peptide of the non-enveloped Flock House virus (FHV), which displays characteristics similar to antimicrobial peptides [37,60,61]. In our previous study, we employed microsecond equilibrium simulations to examine the folding characteristics of γ 1 , on membranes of different compositions [37].…”